I've a specific scaffold with a known binding mode and activity against a particular target, and I want to explore the chemical space around that scaffold by generating a library of compounds with varied functional groups and other molecular fragments used to grow the scaffold further randomly. I know I can do this using Schrodinger, but are there any open freely available softwares or web servers that can do this?
Hi Aditya
I knew a server but unfortunately it has been down for quite some time. Anyway, You can approach this in 2 ways:
1) Either, Use the scaffold to search for molecules having the same scaffold in ZINC 12/ZINC 15. You can do this by ZINCpharmer (http://zincpharmer.csb.pitt.edu/)
2) or ask any of your Chemist friend to rationally design some of the molecules based on the scaffold.
Hi Aditya,
The following web servers may help you:
1) e-LEA3D: ChemInformatic Tools and Databases
http://chemoinfo.ipmc.cnrs.fr/
2) Virtual_combinatorial_library
http://www.cheminfo.org/Chemistry/Cheminformatics/Virtual_combinatorial_library/index.html
Thank you, Yoshinobu Ishikawa! These seem to be quite helpful in general too.
You can do this using the pipelining program KNIME and associated free community contributed chemoinformatics nodes from RDKit, ChemAxon and so on. A desktop version of KNIME is free to use. If you want a server based installation then there is a cost.
https://www.knime.com/
I find KNIME to be an extremely useful free resource for the modeller/chemoinformatician
John
Shradheya Raj Rajeshwar Gupta Stop spamming all CADD related questions on this forum with your copy paste answer evidently trying to promote your server/site. It is not even relevant to the questions asked. I have received around a dozen notifications in the last minutes because of your spam activity.
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